A gene is considered a candidate gene for obesity or type 2 diabetes in Pima Indians if 1) it has a known physiological function in a pathway relevant to type 2 diabetes/obesity or 2) it is associated with diabetes/obesity in another human population or in an animal model. In the past year we have directly sequenced and genotyped all detected variants in more than 50 physiologic candidate genes for associations with BMI or diabetes. Genotyping was performed in two large population based samples of individuals collected from the Gila River Indian Community. One of the investigated genes was KCNQ1. This gene was initially identified as a type 2 diabetes gene in a Chinese population, but it also appears to have a significant role in determining type 2 diabetes, obesity, and early insulin secretion response in Pima Indians. Variants in this gene exhibit parent of origin effects, such that the variants have different effects on disease risk if they were inherited maternally or paternally. Rare variants in genes along the Leptin/Melanocortin pathway cause severe monogenic obesity in childhood; therfore, genes along this pathway were also sequenced as candidate genes for obesity in Pima Indians.Sequenced genes include LEP, LEPR, POMC, MC4R,Sim1 and BDNF. Common variation in LEPR was identified that was reproducibly associated with modest changes in BMI, and the risk allele for overweight was associated with a decrease in energy expenditure measured over 24 hours in a human respiratory chamber. This is the first report of variation in LEPR effecting energy expenditure in humans. Many years ago we first sequenced MC4R in a small number of case/control samples for obesity and identified some missense variants. With the recent advances in sequencing technology, we have now been able to determine the frequency of functional mutations in MC4R in a population-based sample of American Indians who reside on the Gila River Indian Community, and analyze their effects on growth during childhood and adulthood.Sequencing of MC4R in 6760 Pima Indians identified 1 nonsense and 9 missense variants, of which 3 may be private to Pima Indians. We performed in vitro functional studies on each of these variants and found that 6 of the 10 caused decreased MC4R function. These 6 functional mutations occurred in 159 individuals (2.4% of the population). We found a greater rate of body mass accumulation and risk of type 2 diabetes before the age of 20 years in individuals with MC4R deficiency, but did not observe a difference in adulthood, indicating that the effects of these mutations are more apparent during the active growth of childhood. We subsequently determined whether common non-coding variation in/near MC4R also affects BMI in this population. A common haplotype (frequency=0.35) from two independent signals in MC4R was identified which provided evidence for association with BMI in American Indians during both adulthood and childhood. Our longitudinal data with repeated BMI measures allowed a comprehensive assessment for the effect of MC4R on obesity risk over lifetime (age 5-50 years). We also identified a MC4R promoter variant that affects expression in vitro, and showed that it influences risk of obesity in part through a propensity for increased food intake and decreased energy expenditure. Our study was the first to report association between a common variant and ad libitum food intake using an automated vending machine paradigm in a clinical research unit, which provides a more objective, reproducible and accurate measure of food intake than that afforded by methods based on self-report. A recent trans-ancestry meta-analysis GWAS (DIAGRAM) identified seven new loci associated with type 2 diabetes mellitus (T2DM). We assessed replication of the seven lead SNPs and further evaluated these loci for additional signals in American Indians. Two of the seven newly identified variants had nominal evidence for association with T2DM and related traits in American Indians. However, within the LPP locus, a different variant was identified in American Indians which suggests that more than one region may harbor T2DM associated variants at this locus.